Database Commons

a catalog of worldwide biological databases

As a growing number of haplotypic sequences from resequencing studies are now accumulating for Drosophila in the main primary sequence databases, collectively they can now be used to describe the general pattern of nucleotide variation across species and genes of this genus. The Drosophila Polymorphism Database (DPDB) is a secondary database that provides a collection of all well-annotated polymorphic sequences in Drosophila together with their associated diversity measures and options for reanalysis of the data that greatly facilitate both multi-locus and multi-species diversity studies in one of the most important groups of model organisms. Here we describe the state-of-the-art of the DPDB database and provide a step-by-step guide to all its searching and analytic capabilities. Finally, we illustrate its usefulness through selected examples. DPDB is freely available at http://dpdb.uab.cat.

MOTIVATION: Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures.
RESULTS: We define a data model for the storage, representation and analysis of genotypic and haplotypic data. Under this model we have created DPDB, 'Drosophila Polymorphism Database', a web site that provides a daily updated repository of all well-annotated polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity, linkage disequilibrium and codon bias. For data collection, analysis and updating we use PDA, a pipeline that automates the process of sequence retrieval, grouping, alignment and estimation of nucleotide diversity from Genbank sequences in different functional regions. The web site also includes analysis tools for sequence comparison and the estimation of genetic diversity, a page with real-time statistics of the database contents, a help section and a collection of selected links.
AVAILABILITY: DPDB is freely available at http://dpdb.uab.es and can be downloaded via FTP.